Is there a way to set parameters for the Java VM when using a Snakemake wrapper?

Question

When using tools like picard or fgbio through snakemake wrappers, I keep running into out-of-memory issues. At the moment I resort to direct shell calls, which allow me to set the VMs memory. I would prefer to pass these parameters to the wrapped tools. Is there a way, maybe through the resources directive, passing something like mem_mb=10000? I tried, but have not gotten it to work yet.

Answer 1

I have never used the wrapper directive but looking for example at markduplicates/wrapper.py the shell command is picard MarkDuplicates {snakemake.params} .... So maybe using the params slot works?

rule markdups:
    input:
        'in.bam',
    output:
        bam= 'out.bam',
        metrics= 'metrics.tmp',
    params:
        mem= "-Xmx4g",
    wrapper:
        "0.31.0/bio/picard/markduplicates"

picard should understand that -Xmx... is a java parameter.

Answer 2

According to wrapper sources (https://bitbucket.org/snakemake/snakemake-wrappers/src/bd3178f4b82b1856370bb48c8bdbb1932ace6a19/bio/picard/markduplicates/wrapper.py?at=master&fileviewer=file-view-default), it uses cmdline:

from snakemake.shell import shell


shell("picard MarkDuplicates {snakemake.params} INPUT={snakemake.input} "
      "OUTPUT={snakemake.output.bam} METRICS_FILE={snakemake.output.metrics} "
      "&> {snakemake.log}")

So you could pass any options using params: "smth" section.

If you check picard excecutable script sources:

 cat `which picard`

You will find:

...
pass_args=""
for arg in "$@"; do
    case $arg in
        '-D'*)
            jvm_prop_opts="$jvm_prop_opts $arg"
            ;;
        '-XX'*)
            jvm_prop_opts="$jvm_prop_opts $arg"
            ;;
         '-Xm'*)
            jvm_mem_opts="$jvm_mem_opts $arg"
            ;;
         *)
            if [[ ${pass_args} == '' ]] #needed to avoid preceeding space on first arg e.g. ' MarkDuplicates'
            then 
                pass_args="$arg" 
            else
                pass_args="$pass_args \"$arg\"" #quotes later arguments to avoid problem with ()s in MarkDuplicates regex arg
            fi
            ;;
    esac
done
...

So I assume this should work:

rule markdups:
    input:
        "in.bam",
    output:
        bam = "out.bam",
        metrics = "metrics.tmp",
    params:
        "-Xmx10000m"
    wrapper:
        "0.31.0/bio/picard/markduplicates"